• Documents
  • Authors
  • Tables
  • Log in
  • Sign up
  • MetaCart
  • DMCA
  • Donate

CiteSeerX logo

Advanced Search Include Citations
Advanced Search Include Citations

XMIPP: a new generation of an open-source image processing package for electron microscopy. (2004)

by C O S Sorzano
Venue:J. Struct. Biol.
Add To MetaCart

Tools

Sorted by:
Results 1 - 10 of 46
Next 10 →

Maximum-Likelihood Multi-Reference Refinement for Electron Microscopy Images

by Sjors H. W. Scheres, Mikel Valle, Rafael Nuñez, Carlos O. S. Sorzano, Roberto Marabini, Gabor T. Herman, Jose-maria Carazo, Biocomputing Unit Centro, Escuela Politécnica Superior, Escuela Politécnica Superior - J. Molecular Biology , 2005
"... A maximum-likelihood approach to multi-reference image refinement is presented. In contrast to conventional cross-correlation refinement, the new approach includes a formal description of the noise, implying that it is especially suited to cases with low signal-to-noise ratios. Application of this a ..."
Abstract - Cited by 20 (4 self) - Add to MetaCart
A maximum-likelihood approach to multi-reference image refinement is presented. In contrast to conventional cross-correlation refinement, the new approach includes a formal description of the noise, implying that it is especially suited to cases with low signal-to-noise ratios. Application of this approach to a cryo-electron microscopy dataset revealed two major classes for projections of simian virus 40 large T-antigen in complex with an asymmetric DNA-probe, containing the origin of simian virus 40 replication. Strongly bent projections of dodecamers showed density that may be attributed to the complexed double-stranded DNA, while almost straight projections revealed a twist in the relative orientation of the hexameric subunits. This new level of detail for large T-antigen projections was not detected using conventional techniques. For a negative stain dataset, maximum-likelihood refinement yielded results that were practically identical to those obtained using conventional multi-reference refinement. Results obtained using simulated data suggest that the efficiency of the maximum-likelihood approach may be further enhanced by explicitly incorporating the microscope contrast transfer function in the image formation model.

The structure of CCT-Hsc70 NBD suggests a mechanism for Hsp70 delivery of substrates to the chaperonin. Nat Struct Mol Biol 15: 858–864

by Jorge Cuéllar , Jaime Martín-Benito , Sjors H W Scheres , Rui Sousa , Fernando Moro , Eduardo Ló Pez-Viñas , Paulino Gó Mez-Puertas , Arturo Muga , José L Carrascosa , José M Valpuesta , 2008
"... ..."
Abstract - Cited by 7 (0 self) - Add to MetaCart
Abstract not found

Weighted distance transforms generalized to modules and their computation on point lattices.

by Céline Fouard , Robin Strand , Gunilla Borgefors - Centre for Image Analysis, Uppsala University, , 2006
"... Abstract This paper presents the generalization of weighted distances to modules and their computation through the chamfer algorithm on general point lattices. The first part is dedicated to formalization of definitions and properties (distance, metric, norm) of weighted distances on modules. It re ..."
Abstract - Cited by 5 (1 self) - Add to MetaCart
Abstract This paper presents the generalization of weighted distances to modules and their computation through the chamfer algorithm on general point lattices. The first part is dedicated to formalization of definitions and properties (distance, metric, norm) of weighted distances on modules. It resumes tools found in literature to express the weighted distance of any point of a module and to compute optimal weights in the general case to get rotation invariant distances. The second part of this paper proves that, for any point lattice, the sequential two-scan chamfer algorithm produces correct distance maps. Finally, the definitions and computation of weighted distances are applied to the face-centered cubic (FCC) and body-centered cubic (BCC) grids.
(Show Context)

Citation Context

...olume images (i.e. that gives a sequence of 2D slices) such as magnetic resonance imaging (MRI), computed tomography (CT), single photon emission computed tomography (SPECT), or positron emission tomography (PET) can be adjusted to work on the FCC or BCC grids. For SPECT and CT, using the filtered back-projection method or direct Fourier method, the fact that the Fourier transform for the FCC and BCC grids (and for 2D planes that correspond to the 2D slices) exists is enough. Images on the FCC and BCC grids acquired using the algebraic reconstruction technique for SPECT or CT is found in Ref. [10]. They use spherically-symmetric volume elements (blobs) [11]. With the PET technique, the origin of gamma-rays (produced by annihilation of an emitted positron and an electron) are computed. The technique does not depend on the underlying grid except in the digitization step, which just as well can be performed on the FCC and BCC grids. Dealing with digital images means dealing with discrete grids. Indeed, digital images are discrete representation of the continuous world. Two kinds of approaches can be adopted to deal with discrete grids. The first one applies continuous methods to the discr...

Single-particle 3D reconstruction from cryo-electron microscopy images on GPU

by Guangming Tan, Ziyu Guo, Mingyu Chen, Dan Meng - in: Proceedings of the International conference on Supercomputing ICS , 2009
"... Single-particle 3D reconstruction from cryo-electron microscopy (cryo-EM) images is a kernel application of biological molecules analysis, as the computational requirement of which is now beyond PetaFlop for a high-resolution 3D structure. In this paper, we quantitatively analyze the workload, com-p ..."
Abstract - Cited by 3 (3 self) - Add to MetaCart
Single-particle 3D reconstruction from cryo-electron microscopy (cryo-EM) images is a kernel application of biological molecules analysis, as the computational requirement of which is now beyond PetaFlop for a high-resolution 3D structure. In this paper, we quantitatively analyze the workload, com-putational intensity and memory performance of the ap-plication, parallelize it on an emerging multicore architec-ture GPU-CUDA. Further we apply a percolation technique to decouple computation with memory operations and or-chestrate thread-data mapping to reduce the overhead off-chip memory operations. Finally we tested our optimiza-tion strategy on a popular open-source package EMAN to GPU-CUDA, which achieves a relative speedup of about 10X to the original CPU-only EMAN. The experimental results also show that the proposed percolation program-ming greatly improves utilization of memory bandwidth and floating-point units.
(Show Context)

Citation Context

... to cope with these increasing computational efforts, most of these software packages have implemented parallel reconstruction algorithms to be used on various conventional parallel computing systems =-=[15, 8, 2, 22]-=-. Electron microscopy data are typically well suited for parallelization, since both images and processes can be treated independently, e.g. electron micrographs can be backprojected in a common three...

Molecular architecture of a multifunctional MCM complex

by June Sanchez-berrondo, Pablo Mesa, Arkaitz Ibarra, Maria I. Martínez-jiménez, Luis Blanco, Juan Méndez, Jasminka Boskovic, Guillermo Montoya , 2011
"... DNA replication is strictly regulated through a sequence of steps that involve many macromolecular protein complexes. One of them is the replicative helicase, which is required for initiation and elongation phases. A MCM helicase found as a prophage in the genome of Bacillus cereus is fused with a p ..."
Abstract - Cited by 2 (0 self) - Add to MetaCart
DNA replication is strictly regulated through a sequence of steps that involve many macromolecular protein complexes. One of them is the replicative helicase, which is required for initiation and elongation phases. A MCM helicase found as a prophage in the genome of Bacillus cereus is fused with a primase domain constituting an integrative arrangement of two essential activities for replication. We have isolated this helicase–primase complex (BcMCM) showing that it can bind DNA and displays not only helicase and primase but also DNA polymerase activity. Using single-particle electron microscopy and 3D reconstruction, we obtained structures of BcMCM using ATPcS or ADP in the absence and presence of DNA. The complex depicts the typical hexameric ring shape. The dissection of the unwinding mechanism using site-directed mutagenesis in the Walker A, Walker B, arginine finger and the helicase channels, suggests that the BcMCM complex unwinds DNA following the extrusion model similarly to the E1 helicase from papillomavirus.
(Show Context)

Citation Context

...ed, bandpass filtered, centered, normalized and subjected to angular refinement. The raw data was analysed using reference-free alignment and classification methods implemented in EMAN (29) and XMIPP =-=(30)-=-. An initial 3D template for refinement was built using ‘startscym’ program implemented in EMAN (29) and the 6-fold symmetry of the molecule. BcMCM–ADP–ssDNA complex was obtained by incubating, in hex...

Cryo X-ray nano-tomography of vaccinia virus infected cells

by Francisco Javier Chichón , Maria Josefa Rodríguez , Eva Pereiro , Michele Chiappi , Beatriz Perdiguero , Peter Guttmann , Stephan Werner , Stefan Rehbein , Gerd Schneider , Mariano Esteban , José L Carrascosa - J. Struct. Biol
"... a b s t r a c t We have performed full-field cryo X-ray microscopy in the water window photon energy range on vaccinia virus (VACV) infected cells to produce tomographic reconstructions. PtK2 cells were infected with a GFP-expressing VACV strain and frozen by plunge fast freezing. The infected cell ..."
Abstract - Cited by 2 (1 self) - Add to MetaCart
a b s t r a c t We have performed full-field cryo X-ray microscopy in the water window photon energy range on vaccinia virus (VACV) infected cells to produce tomographic reconstructions. PtK2 cells were infected with a GFP-expressing VACV strain and frozen by plunge fast freezing. The infected cells were selected by light fluorescence microscopy of the GFP marker and subsequently imaged in the X-ray microscope under cryogenic conditions. Tomographic tilt series of X-ray images were used to yield three-dimensional reconstructions showing different cell organelles (nuclei, mitochondria, filaments), together with other structures derived from the virus infection. Among them, it was possible to detect viral factories and two types of viral particles related to different maturation steps of VACV (immature and mature particles), which were compared to images obtained by standard electron microscopy of the same type of cells. In addition, the effect of radiation damage during X-ray tomographic acquisition was analyzed. Thin sections studied by electron microscopy revealed that the morphological features of the cells do not present noticeable changes after irradiation. Our findings show that cryo X-ray nano-tomography is a powerful tool for collecting three-dimensional structural information from frozen, unfixed, unstained whole cells with sufficient resolution to detect different virus particles exhibiting distinct maturation levels.
(Show Context)

Citation Context

...ate objective with an outermost zone width of drn = 40 nm, whereas a zone plate with drn = 25 nm was used for the acquisition of 4 datasets. The effective pixel sizes in the images were 15.6 nm or 8.6 nm (with the 40 nm zone plate objective, depending on the magnification), and 9.7 nm (with the 25 nm objective). The image stacks were pre-processed to normalize and correct the intensity distribution delivered to the sample by the capillary condenser using flat field images in a program developed for XMIPP3.0 software package (Marabini et al., 1996; Scheres et al., 2008; Schneider et al., 2010; Sorzano et al., 2004). Alignment of the tilted series was done with IMOD (Kremer et al., 1996), and the final reconstructions were performed using the iterative SIRT reconstruction option in TOMO3D (Agulleiro and Fernandez, 2011). To enhance the signal to noise levels we used TOMOBFLOW (Fernandez, 2009). The visualization and segmentation of the final volumes was carried out in Amira, IMOD and Chimera (Pettersen et al., 2004). The 3D-resolution estimation was done using the same approach as in Carrascosa et al. (2009). 2.6. Standard embedding For ultrastructural studies under electron microscopy, cells were cultu...

Grid Computing in 3D-EM Image Processing using Xmipp

by S. H. W. Scheres, A. J. Merino, C. O. S. Sorzano, J. M. Carazo
"... * These authors contributed equally to this work Image processing in three-dimensional electron microscopy (3D-EM) is characterized by large amounts of data, and voluminous computing requirements. Here, we report our first experience with grid computing in this area. We present an interface between ..."
Abstract - Cited by 1 (0 self) - Add to MetaCart
* These authors contributed equally to this work Image processing in three-dimensional electron microscopy (3D-EM) is characterized by large amounts of data, and voluminous computing requirements. Here, we report our first experience with grid computing in this area. We present an interface between grid computing middleware and our image processing package Xmipp. The efficacy of this approach was illustrated with an Xmipp application for estimation of the contrast transfer function. In addition, we report our experience with grid computing in the development of a novel image refinement algorithm based on maximum likelihood principles. Its extensive CPUrequirements might have seriously hampered the algorithm development, if not for the farreaching resources of grid computing. Our results suggest that electron microscopy image processing may be particularly well suited for grid computing. 1.
(Show Context)

Citation Context

...orted [3, 4]. But, so far the use of grids in 3D-EM has been limited. Over the past eight years, our group has been developing a program package for singleparticle 3D-EM image processing called Xmipp =-=[5]-=-. Whereas up to now its approach to highperformance computing has been based on MPI (message passing interface) implementations of the most time-consuming algorithms, current efforts have also address...

Computational Inversion of Electron Tomography Images Using L2-Gradient Flows ∗

by Guoliang Xu, Ming Li, Ajay Gopinath Ch, Rajit Bajaj
"... In this paper, we present a stable, reliable and robust method for reconstructing a three dimensional density function from a set of two dimensional electric tomographic images. By minimizing an energy functional consisting of a fidelity term and a regularization term, an L2-gradient flow is derived ..."
Abstract - Cited by 1 (1 self) - Add to MetaCart
In this paper, we present a stable, reliable and robust method for reconstructing a three dimensional density function from a set of two dimensional electric tomographic images. By minimizing an energy functional consisting of a fidelity term and a regularization term, an L2-gradient flow is derived. The flow is integrated by a finite element method in the spatial direction and an explicit Euler scheme in temporal direction. The experimental results show that the proposed method is efficient and effective.
(Show Context)

Citation Context

...ts the L2-errors now in the presence of noise. Where the exact function to be projected is 17 defined by (7.1). In order to add Gaussian noise with the given signal-to-noise ratio (SNR), we use xmipp =-=[15]-=- package to compute the standard deviation for each given SNR value and then use the standard deviation to add Gaussian noise to each projection. For instance, for a SNR of 0.33, a total noise with a ...

Cryoelectron Microscopy of Icosahedral Virus Particles

by Wen Jiang, Wah Chiu
"... With the rapid progresses in both instrumentation and computing, it is increasingly straightforward and routine to determine the structures of icosahedral viruses to subnano-meter resolutions (6–10 Å) by cryoelectron microscopy and image reconstruction. In this resolution range, secondary structure ..."
Abstract - Cited by 1 (0 self) - Add to MetaCart
With the rapid progresses in both instrumentation and computing, it is increasingly straightforward and routine to determine the structures of icosahedral viruses to subnano-meter resolutions (6–10 Å) by cryoelectron microscopy and image reconstruction. In this resolution range, secondary structure elements of protein subunits can be clearly dis-cerned. Combining the three-dimensional density map and bioinformatics of the protein components, the folds of the virus capsid shell proteins can be derived. This chapter will describe the experimental and computational procedures that lead to subnanometer resolu-tion structural determinations of icosahedral virus particles. In addition, we will describe how to extract useful structural information from the three-dimensional maps. Key Words: Cryo-EM; cryoelectron microscopy; icosahedral virus; 3D reconstruction; subnanometer resolution; secondary structure elements; structural fitting 1.
(Show Context)

Citation Context

...ction The 3D reconstruction of icosahedral viruses was first introduced by Crowther et al. (1,2). There are numerous software packages such as Spider (30), IMAGIC (31), Frealign (32), PFT (33), XMIPP =-=(34)-=-, IMIRS (35), SAVR (11), and EMAN Fig. 3. Examples of particle selection. (A) automatically selected particles. (B) selected particles after manual screening. Cryo-EM of Viruses 353 Fig. 4. Contrast t...

To

by Stephen David Jones , 2014
"... ive rsi ty of ..."
Abstract - Add to MetaCart
ive rsi ty of
(Show Context)

Citation Context

...pid construction of detailed models. The software packages mentioned above all assume the creation of a particular immutable model as their goal. As an example consider a script written for the XMIPP =-=[156, 157, 158]-=- text based phantom creation tool. An identical three dimensional model will be created each time the script is run because the script is unable to facilitate random effects in synthesised models. The...

Powered by: Apache Solr
  • About CiteSeerX
  • Submit and Index Documents
  • Privacy Policy
  • Help
  • Data
  • Source
  • Contact Us

Developed at and hosted by The College of Information Sciences and Technology

© 2007-2019 The Pennsylvania State University